Tools for Phylogenomic Exploration within and Among Clade-Oriented Databases

Putting comparative evolutionary perspectives into a form that may be used successfully in translational applications such as plant breeding presents significant challenges of user interface design. This is due in part to the wide range of scales involved when navigating from relatively broad regions defined by family and population-based recombinant mapping approaches, and in part to the distributed and heterogeneous nature of the databases that maintain much of the information relevant to the goals of the users. We have explored this problem space in the development of genomic-context and gene-family oriented displays in the Legume Information System’s new site at legumeinfo.org. Using community-standard plant gene families from Phytozome and open-source tools from GMOD as our starting point, we have developed methodologies for augmenting the initial gene family definitions with annotations from species of interest to our user community, for importing phylogenomic data into the Chado database framework, and for presenting the data in dynamic and intuitive web-based interfaces for search and display. By using gene trees as a navigational guide to schematic representations of gene order and orientation, users are provided with significant levels of information content “at a glance”; by handling sequences of gene family memberships as a unit of search and comparison, the user interface is made sufficiently responsive to enable quick assessment of the levels of conservation, novelty, and various type of structural events that can serve to direct the user to more detailed explorations at finer levels of granularity in other tools and within other sites.